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Kok LC, Tsai CC, Liao YH, Lo YL, Cheng NW, Lin CT, Chang HY. Roles of transcriptional factor PsrA in the regulation of quorum sensing in Pseudomonas aeruginosa PAO1. Front Microbiol 2024; 15:1424330. [PMID: 38989021 PMCID: PMC11233452 DOI: 10.3389/fmicb.2024.1424330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024] Open
Abstract
The transcription factor PsrA regulates fatty acid metabolism, the type III secretion system, and quinolone signaling quorum sensing system in Pseudomonas aeruginosa. To explore additional roles of PsrA in P. aeruginosa, this study engineered a P. aeruginosa PAO1 strain to carry a recombinant plasmid with the psrA gene (pMMBpsrA) and examined the impact of elevated psrA expression to the bacterium. Transcriptomic analysis revealed that PsrA significantly downregulated genes encoding the master quorum-sensing regulators, RhlR and LasR, and influenced many quorum-sensing-associated genes. The role of PsrA in quorum sensing was further corroborated by testing autoinducer synthesis in PAO1 [pMMBpsrA] using two reporter bacteria strains Chromobacterium violaceum CV026 and Escherichia coli [pSB1075], which respond to short- and long-chain acyl homoserine lactones, respectively. Phenotypic comparisons of isogenic ΔpsrA, ΔlasR, and ΔpsrAΔlasR mutants revealed that the reduced elastase, caseinase, and swarming activity in PAO1 [pMMBpsrA] were likely mediated through LasR. Additionally, electrophoretic mobility shift assays demonstrated that recombinant PsrA could bind to the lasR promoter at a 5'-AAACGTTTGCTT-3' sequence, which displays moderate similarity to the previously reported consensus PsrA binding motif. Furthermore, the PsrA effector molecule oleic acid inhibited PsrA binding to the lasR promoter and restored several quorum sensing-related phenotypes to wild-type levels. These findings suggest that PsrA regulates certain quorum-sensing phenotypes by negatively regulating lasR expression, with oleic acid acting as a crucial signaling molecule.
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Affiliation(s)
- Li-Ching Kok
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City, Taiwan
| | - Chia-Chun Tsai
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City, Taiwan
| | - Yu-Hsuan Liao
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City, Taiwan
| | - Yi-Ling Lo
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City, Taiwan
| | - Nai-Wei Cheng
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City, Taiwan
| | - Ching-Ting Lin
- School of Chinese Medicine, China Medical University, Taichung City, Taiwan
| | - Hwan-You Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City, Taiwan
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2
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Zhu Y, Luo B, Mou X, Song Y, Zhou Y, Luo Y, Sun B, Luo Y, Tang H, Su Z, Bao R. Pseudomonas aeruginosa regulator PvrA binds simultaneously to multiple pseudo-palindromic sites for efficient transcription activation. SCIENCE CHINA. LIFE SCIENCES 2024; 67:900-912. [PMID: 37938507 DOI: 10.1007/s11427-022-2363-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/10/2023] [Indexed: 11/09/2023]
Abstract
Tetracycline repressor (TetR) family regulators (TFRs) are the largest group of DNA-binding transcription factors and are widely distributed in bacteria and archaea. TFRs play vital roles in controlling the expression of various genes and regulating diverse physiological processes. Recently, a TFR protein Pseudomonas virulence regulator A (PvrA), was identified from Pseudomonas aeruginosa as the transcriptional activator of genes involved in fatty acid utilization and bacterial virulence. Here, we show that PvrA can simultaneously bind to multiple pseudo-palindromic sites and upregulate the expression levels of target genes. Cryo-electron microscopy (cryo-EM) analysis indicates the simultaneous DNA recognition mechanism of PvrA and suggests that the bound DNA fragments consist of a distorted B-DNA double helix. The crystal structure and functional analysis of PvrA reveal a hinge region that secures the correct domain motion for recognition of the promiscuous promoter. Additionally, our results showed that mutations disrupting the regulatory hinge region have differential effects on biofilm formation and pyocyanin biosynthesis, resulting in attenuated bacterial virulence. Collectively, these findings will improve the understanding of the relationship between the structure and function of the TetR family and provide new insights into the mechanism of regulation of P. aeruginosa virulence.
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Affiliation(s)
- Yibo Zhu
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- Accurate Biotechnology (Hunan) Co., Ltd, Changsha, 410006, China
| | - Bingnan Luo
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xingyu Mou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yingjie Song
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Yonghong Zhou
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, 850000, China
| | - Yongbo Luo
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Youfu Luo
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hong Tang
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Zhaoming Su
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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3
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Graham CI, MacMartin TL, de Kievit TR, Brassinga AKC. Molecular regulation of virulence in Legionella pneumophila. Mol Microbiol 2024; 121:167-195. [PMID: 37908155 DOI: 10.1111/mmi.15172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 11/02/2023]
Abstract
Legionella pneumophila is a gram-negative bacteria found in natural and anthropogenic aquatic environments such as evaporative cooling towers, where it reproduces as an intracellular parasite of cohabiting protozoa. If L. pneumophila is aerosolized and inhaled by a susceptible person, bacteria may colonize their alveolar macrophages causing the opportunistic pneumonia Legionnaires' disease. L. pneumophila utilizes an elaborate regulatory network to control virulence processes such as the Dot/Icm Type IV secretion system and effector repertoire, responding to changing nutritional cues as their host becomes depleted. The bacteria subsequently differentiate to a transmissive state that can survive in the environment until a replacement host is encountered and colonized. In this review, we discuss the lifecycle of L. pneumophila and the molecular regulatory network that senses nutritional depletion via the stringent response, a link to stationary phase-like metabolic changes via alternative sigma factors, and two-component systems that are homologous to stress sensors in other pathogens, to regulate differentiation between the intracellular replicative phase and more transmissible states. Together, we highlight how this prototypic intracellular pathogen offers enormous potential in understanding how molecular mechanisms enable intracellular parasitism and pathogenicity.
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Affiliation(s)
- Christopher I Graham
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teassa L MacMartin
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teresa R de Kievit
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ann Karen C Brassinga
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
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4
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Schiaffi V, Barras F, Bouveret E. Matching the β-oxidation gene repertoire with the wide diversity of fatty acids. Curr Opin Microbiol 2024; 77:102402. [PMID: 37992547 DOI: 10.1016/j.mib.2023.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/24/2023]
Abstract
Bacteria can use fatty acids (FAs) from their environment as carbon and energy source. This catabolism is performed by the enzymes of the well-known β-oxidation machinery, producing reducing power and releasing acetyl-CoA that can feed the tricarboxylic acid cycle. FAs are extremely diverse: they can be saturated or (poly)unsaturated and are found in different sizes. The need to degrade such a wide variety of compounds may explain why so many seemingly homologous enzymes are found for each step of the β-oxidation cycle. In addition, the degradation of unsaturated fatty acids requires specific auxiliary enzymes for isomerase and reductase reactions. Furthermore, the β-oxidation cycle can be blocked by dead-end products, which are taken care of by acyl-CoA thioesterases. Yet, the functional characterization of the enzymes required for the degradation of the full diversity of FAs remains to be documented in most bacteria.
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Affiliation(s)
- Veronica Schiaffi
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France
| | - Frédéric Barras
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France
| | - Emmanuelle Bouveret
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France.
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5
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Degradation of Exogenous Fatty Acids in Escherichia coli. Biomolecules 2022; 12:biom12081019. [PMID: 35892328 PMCID: PMC9329746 DOI: 10.3390/biom12081019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Many bacteria possess all the machineries required to grow on fatty acids (FA) as a unique source of carbon and energy. FA degradation proceeds through the β-oxidation cycle that produces acetyl-CoA and reduced NADH and FADH cofactors. In addition to all the enzymes required for β-oxidation, FA degradation also depends on sophisticated systems for its genetic regulation and for FA transport. The fact that these machineries are conserved in bacteria suggests a crucial role in environmental conditions, especially for enterobacteria. Bacteria also possess specific enzymes required for the degradation of FAs from their environment, again showing the importance of this metabolism for bacterial adaptation. In this review, we mainly describe FA degradation in the Escherichia coli model, and along the way, we highlight and discuss important aspects of this metabolism that are still unclear. We do not detail exhaustively the diversity of the machineries found in other bacteria, but we mention them if they bring additional information or enlightenment on specific aspects.
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Blunt W, Blanchard C, Morley K. Effects of environmental parameters on microbial rhamnolipid biosynthesis and bioreactor strategies for enhanced productivity. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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7
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Price CL, Warrilow AGS, Rolley NJ, Parker JE, Thoss V, Kelly DE, Corcionivoschi N, Kelly SL. Cytochrome P450 168A1 from Pseudomonas aeruginosa is involved in the hydroxylation of biologically relevant fatty acids. PLoS One 2022; 17:e0265227. [PMID: 35312722 PMCID: PMC8936499 DOI: 10.1371/journal.pone.0265227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 02/24/2022] [Indexed: 11/26/2022] Open
Abstract
The cytochrome P450 CYP168A1 from Pseudomonas aeruginosa was cloned and expressed in Escherichia coli followed by purification and characterization of function. CYP168A1 is a fatty acid hydroxylase that hydroxylates saturated fatty acids, including myristic (0.30 min-1), palmitic (1.61 min-1) and stearic acids (1.24 min-1), at both the ω-1- and ω-2-positions. However, CYP168A1 only hydroxylates unsaturated fatty acids, including palmitoleic (0.38 min-1), oleic (1.28 min-1) and linoleic acids (0.35 min-1), at the ω-1-position. CYP168A1 exhibited a catalytic preference for palmitic, oleic and stearic acids as substrates in keeping with the phosphatidylcholine-rich environment deep in the lung that is colonized by P. aeruginosa.
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Affiliation(s)
- Claire L. Price
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Andrew G. S. Warrilow
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Nicola J. Rolley
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Josie E. Parker
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Vera Thoss
- Plant Chemistry Group, School of Chemistry, Bangor University, Bangor, Gwynedd, Wales, United Kingdom
| | - Diane E. Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Nicolae Corcionivoschi
- Agri-Food and Biosciences Institute, Veterinary Science Division, Bacteriology Branch, Stoney Road, Stormont, Belfast, Northern Ireland, United Kingdom
- Faculty of Bioengineering of Animal Resources, Banat University of Agricultural Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
| | - Steven L. Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
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8
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Cell Envelope Stress Response in Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:147-184. [DOI: 10.1007/978-3-031-08491-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Allsopp LP, Collins ACZ, Hawkins E, Wood TE, Filloux A. RpoN/Sfa2-dependent activation of the Pseudomonas aeruginosa H2-T6SS and its cognate arsenal of antibacterial toxins. Nucleic Acids Res 2021; 50:227-243. [PMID: 34928327 PMCID: PMC8855297 DOI: 10.1093/nar/gkab1254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/26/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa uses three type six secretion systems
(H1-, H2- and H3-T6SS) to manipulate its environment, subvert host cells and for
microbial competition. These T6SS machines are loaded with a variety of
effectors/toxins, many being associated with a specific VgrG. How P.
aeruginosa transcriptionally coordinates the main T6SS clusters and
the multiple vgrG islands spread through the genome is unknown.
Here we show an unprecedented level of control with RsmA repressing most known
T6SS-related genes. Moreover, each of the H2- and H3-T6SS clusters encodes a
sigma factor activator (SFA) protein
called, Sfa2 and Sfa3, respectively. SFA proteins are enhancer binding proteins
necessary for the sigma factor RpoN. Using a combination of RNA-seq, ChIP-seq
and molecular biology approaches, we demonstrate that RpoN coordinates the T6SSs
of P. aeruginosa by activating the H2-T6SS but repressing the
H1- and H3-T6SS. Furthermore, RpoN and Sfa2 control the expression of the
H2-T6SS-linked VgrGs and their effector arsenal to enable very effective
interbacterial killing. Sfa2 is specific as Sfa3 from the H3-T6SS cannot
complement loss of Sfa2. Our study further delineates the regulatory mechanisms
that modulate the deployment of an arsenal of T6SS effectors likely enabling
P. aeruginosa to adapt to a range of environmental
conditions.
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Affiliation(s)
- Luke P Allsopp
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Alice C Z Collins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Eleanor Hawkins
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Thomas E Wood
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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10
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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11
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Graham CI, Patel PG, Tanner JR, Hellinga J, MacMartin TL, Hausner G, Brassinga AKC. Autorepressor PsrA is required for optimal Legionella pneumophila growth in Acanthamoeba castellanii protozoa. Mol Microbiol 2021; 116:624-647. [PMID: 34018265 DOI: 10.1111/mmi.14760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/16/2021] [Accepted: 05/16/2021] [Indexed: 11/26/2022]
Abstract
Legionella pneumophila possesses a unique intracellular lifecycle featuring distinct morphological stages that include replicative forms and transmissive cyst forms. Expression of genes associated with virulence traits and cyst morphogenesis is concomitant, and governed by a complex stringent response based-regulatory network and the stationary phase sigma factor RpoS. In Pseudomonas spp., rpoS expression is controlled by the autorepressor PsrA, and orthologs of PsrA and RpoS are required for cyst formation in Azotobacter. Here we report that the L. pneumophila psrA ortholog, expressed as a leaderless monocistronic transcript, is also an autorepressor, but is not a regulator of rpoS expression. Further, the binding site sequence recognized by L. pneumophila PsrA is different from that of Pseudomonas PsrA, suggesting a repertoire of target genes unique to L. pneumophila. While PsrA was dispensable for growth in human U937-derived macrophages, lack of PsrA affected bacterial intracellular growth in Acanthamoeba castellanii protozoa, but also increased the quantity of poly-3-hydroxybutyrate (PHB) inclusions in matured transmissive cysts. Interestingly, overexpression of PsrA increased the size and bacterial load of the replicative vacuole in both host cell types. Taken together, we report that PsrA is a host-specific requirement for optimal temporal progression of L. pneumophila intracellular lifecycle in A. castellanii.
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Affiliation(s)
- Christopher I Graham
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
| | - Palak G Patel
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
| | - Jennifer R Tanner
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
| | - Jacqueline Hellinga
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
| | - Teassa L MacMartin
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
| | - Georg Hausner
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
| | - Ann Karen C Brassinga
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
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12
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Ackermann YS, Li WJ, Op de Hipt L, Niehoff PJ, Casey W, Polen T, Köbbing S, Ballerstedt H, Wynands B, O'Connor K, Blank LM, Wierckx N. Engineering adipic acid metabolism in Pseudomonas putida. Metab Eng 2021; 67:29-40. [PMID: 33965615 DOI: 10.1016/j.ymben.2021.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/12/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022]
Abstract
Bio-upcycling of plastics is an upcoming alternative approach for the valorization of diverse polymer waste streams that are too contaminated for traditional recycling technologies. Adipic acid and other medium-chain-length dicarboxylates are key components of many plastics including polyamides, polyesters, and polyurethanes. This study endows Pseudomonas putida KT2440 with efficient metabolism of these dicarboxylates. The dcaAKIJP genes from Acinetobacter baylyi, encoding initial uptake and activation steps for dicarboxylates, were heterologously expressed. Genomic integration of these dca genes proved to be a key factor in efficient and reliable expression. In spite of this, adaptive laboratory evolution was needed to connect these initial steps to the native metabolism of P. putida, thereby enabling growth on adipate as sole carbon source. Genome sequencing of evolved strains revealed a central role of a paa gene cluster, which encodes parts of the phenylacetate metabolic degradation pathway with parallels to adipate metabolism. Fast growth required the additional disruption of the regulator-encoding psrA, which upregulates redundant β-oxidation genes. This knowledge enabled the rational reverse engineering of a strain that can not only use adipate, but also other medium-chain-length dicarboxylates like suberate and sebacate. The reverse engineered strain grows on adipate with a rate of 0.35 ± 0.01 h-1, reaching a final biomass yield of 0.27 ± 0.00 gCDW gadipate-1. In a nitrogen-limited medium this strain produced polyhydroxyalkanoates from adipate up to 25% of its CDW. This proves its applicability for the upcycling of mixtures of polymers made from fossile resources into biodegradable counterparts.
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Affiliation(s)
- Yannic S Ackermann
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Wing-Jin Li
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Leonie Op de Hipt
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Paul-Joachim Niehoff
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - William Casey
- Bioplastech Ltd., NovaUCD, Belfield Innovation Park, University College Dublin, Dublin, Ireland
| | - Tino Polen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Sebastian Köbbing
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Hendrik Ballerstedt
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Kevin O'Connor
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland; BiOrbic Bioeconomy SFI Research Centre, University College Dublin, Dublin, Ireland
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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13
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Velázquez-Sánchez C, Vences-Guzmán MÁ, Moreno S, Tinoco-Valencia R, Espín G, Guzmán J, Sahonero-Canavesi DX, Sohlenkamp C, Segura D. PsrA positively regulates the unsaturated fatty acid synthesis operon fabAB in Azotobacter vinelandii. Microbiol Res 2021; 249:126775. [PMID: 33964629 DOI: 10.1016/j.micres.2021.126775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/12/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
In Pseudomonas spp. PsrA, a transcriptional activator of the rpoS gene, regulates fatty acid catabolism by repressing the fadBA5 β-oxidation operon. In Azotobacter vinelandii, a soil bacterium closely related to Pseudomonas species, PsrA is also an activator of rpoS expression, although its participation in the regulation of lipid metabolism has not been analyzed. In this work we found that inactivation of psrA had no effect on the expression of β-oxidation genes in this bacterium, but instead decreased expression of the unsaturated fatty acid biosynthetic operon fabAB (3-hydroxydecanoyl-ACP dehydratase/isomerase and 3-ketoacyl-ACP synthase I). This inactivation also reduced the unsaturated fatty acid content, as revealed by the thin-layer chromatographic analysis, and confirmed by gas chromatography; notably, there was also a lower content of cyclopropane fatty acids, which are synthesized from unsaturated fatty acids. The absence of PsrA has no effect on the growth rate, but showed loss of cell viability during long-term growth, in accordance with the role of these unsaturated and cyclopropane fatty acids in the protection of membranes. Finally, an electrophoretic mobility shift assay revealed specific binding of PsrA to the fabA promoter region, where a putative binding site for this regulator was located. Taken together, our data show that PsrA plays an important role in the regulation of unsaturated fatty acids metabolism in A. vinelandii by positively regulating fabAB.
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Affiliation(s)
- Claudia Velázquez-Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | | | - Soledad Moreno
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Raunel Tinoco-Valencia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Josefina Guzmán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | | | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Segura
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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14
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Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing. J Bacteriol 2021; 203:JB.00432-20. [PMID: 33257523 DOI: 10.1128/jb.00432-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/18/2020] [Indexed: 12/30/2022] Open
Abstract
Gene essentiality studies have been performed on numerous bacterial pathogens, but essential gene sets have been determined for only a few plant-associated bacteria. Pseudomonas protegens Pf-5 is a plant-commensal, biocontrol bacterium that can control disease-causing pathogens on a wide range of crops. Work on Pf-5 has mostly focused on secondary metabolism and biocontrol genes, but genome-wide approaches such as high-throughput transposon mutagenesis have not yet been used for this species. In this study, we generated a dense P. protegens Pf-5 transposon mutant library and used transposon-directed insertion site sequencing (TraDIS) to identify 446 genes essential for growth on rich media. Genes required for fundamental cellular machinery were enriched in the essential gene set, while genes related to nutrient biosynthesis, stress responses, and transport were underrepresented. The majority of Pf-5 essential genes were part of the P. protegens core genome. Comparison of the essential gene set of Pf-5 with those of two plant-associated pseudomonads, P. simiae and P. syringae, and the well-studied opportunistic human pathogen P. aeruginosa PA14 showed that the four species share a large number of essential genes, but each species also had uniquely essential genes. Comparison of the Pf-5 in silico-predicted and in vitro-determined essential gene sets highlighted the essential cellular functions that are over- and underestimated by each method. Expanding essentiality studies into bacteria with a range of lifestyles may improve our understanding of the biological processes important for bacterial survival and growth.IMPORTANCE Essential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens but only a few plant-associated bacteria. Employing genome-wide approaches, such as transposon insertion sequencing, allows for the concurrent analyses of all genes of a bacterial species and rapid determination of essential gene sets. We have used transposon insertion sequencing to systematically analyze thousands of Pseudomonas protegens Pf-5 genes and gain insights into gene functions and interactions that are not readily available using traditional methods. Comparing Pf-5 essential genes with those of three other pseudomonads highlights how gene essentiality varies between closely related species.
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15
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Juárez-Rodríguez MM, Cortes-López H, García-Contreras R, González-Pedrajo B, Díaz-Guerrero M, Martínez-Vázquez M, Rivera-Chávez JA, Soto-Hernández RM, Castillo-Juárez I. Tetradecanoic Acids With Anti-Virulence Properties Increase the Pathogenicity of Pseudomonas aeruginosa in a Murine Cutaneous Infection Model. Front Cell Infect Microbiol 2021; 10:597517. [PMID: 33585272 PMCID: PMC7876447 DOI: 10.3389/fcimb.2020.597517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022] Open
Abstract
Blocking virulence is a promising alternative to counteract Pseudomonas aeruginosa infections. In this regard, the phenomenon of cell-cell communication by quorum sensing (QS) is an important anti-virulence target. In this field, fatty acids (FA) have gained notoriety for their role as autoinducers, as well as anti-virulence molecules in vitro, like some saturated FA (SAFA). In this study, we analyzed the anti-virulence activity of SAFA with 12 to18 carbon atoms and compared their effect with the putative autoinducer cis-2-decenoic acid (CDA). The effect of SAFA on six QS-regulated virulence factors and on the secretion of the exoenzyme ExoU was evaluated. In addition, a murine cutaneous infection model was used to determine their influence on the establishment and damage caused by P. aeruginosa PA14. Dodecanoic (lauric, C12:0) and tetradecanoic (myristic, C14:0) acids (SAFA C12-14) reduced the production of pyocyanin by 35-58% at 40 and 1,000 µM, while CDA inhibited it 62% at a 3.1 µM concentration. Moreover, the SAFA C12-14 reduced swarming by 90% without affecting biofilm formation. In contrast, CDA reduced the biofilm by 57% at 3 µM but did not affect swarming. Furthermore, lauric and myristic acids abolished ExoU secretion at 100 and 50 µM respectively, while CDA reduced it by ≈ 92% at 100 µM. Remarkably, the coadministration of myristic acid (200 and 1,000 µM) with P. aeruginosa PA14 induced greater damage and reduced survival of the animals up to 50%, whereas CDA to 500 µM reduced the damage without affecting the viability of the PA14 strain. Hence, our results show that SAFA C12-14 and CDA have a role in regulation of P. aeruginosa virulence, although their inhibition/activation molecular mechanisms are different in complex environments such as in vivo systems.
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Affiliation(s)
| | - Humberto Cortes-López
- Laboratorio de Fitoquímica, Posgrado de Botánica, Colegio de Postgraduados, Texcoco, Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Bertha González-Pedrajo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Miguel Díaz-Guerrero
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mariano Martínez-Vázquez
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José Alberto Rivera-Chávez
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Israel Castillo-Juárez
- Laboratorio de Fitoquímica, Posgrado de Botánica, Colegio de Postgraduados, Texcoco, Mexico
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16
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Mezzina MP, Manoli MT, Prieto MA, Nikel PI. Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates. Biotechnol J 2020; 16:e2000165. [PMID: 33085217 DOI: 10.1002/biot.202000165] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/16/2020] [Indexed: 12/16/2022]
Abstract
Growing environmental concern sparks renewed interest in the sustainable production of (bio)materials that can replace oil-derived goods. Polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in the central metabolism of producer bacteria, as they act as dynamic reservoirs of carbon and reducing equivalents. PHAs continue to attract industrial attention as a starting point toward renewable, biodegradable, biocompatible, and versatile thermoplastic and elastomeric materials. Pseudomonas species have been known for long as efficient biopolymer producers, especially for medium-chain-length PHAs. The surge of synthetic biology and metabolic engineering approaches in recent years offers the possibility of exploiting the untapped potential of Pseudomonas cell factories for the production of tailored PHAs. In this article, an overview of the metabolic and regulatory circuits that rule PHA accumulation in Pseudomonas putida is provided, and approaches leading to the biosynthesis of novel polymers (e.g., PHAs including nonbiological chemical elements in their structures) are discussed. The potential of novel PHAs to disrupt existing and future market segments is closer to realization than ever before. The review is concluded by pinpointing challenges that currently hinder the wide adoption of bio-based PHAs, and strategies toward programmable polymer biosynthesis from alternative substrates in engineered P. putida strains are proposed.
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Affiliation(s)
- Mariela P Mezzina
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
| | - María Tsampika Manoli
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas «Margarita Salas» (CIB-CSIC), Polymer Biotechnology Group, Madrid, 28040, Spain.,Spanish National Research Council (SusPlast-CSIC), Interdisciplinary Platform for Sustainable Plastics Toward a Circular Economy, Madrid, 28040, Spain
| | - M Auxiliadora Prieto
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas «Margarita Salas» (CIB-CSIC), Polymer Biotechnology Group, Madrid, 28040, Spain.,Spanish National Research Council (SusPlast-CSIC), Interdisciplinary Platform for Sustainable Plastics Toward a Circular Economy, Madrid, 28040, Spain
| | - Pablo I Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
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17
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Xu H, Su Z, Li W, Deng Y, He ZG. MmbR, a master transcription regulator that controls fatty acid β-oxidation genes in Mycolicibacterium smegmatis. Environ Microbiol 2020; 23:1096-1114. [PMID: 32985741 DOI: 10.1111/1462-2920.15249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 11/29/2022]
Abstract
An unusually high lipid content and a complex lipid profile are the most distinctive features of the mycobacterial cell envelope. However, our understanding of the regulatory mechanism underlying mycobacterial lipid metabolism is limited, and the major regulators responsible for lipid homeostasis remain to be characterized. Here, we identified MmbR as a novel master regulator that is essential for maintaining lipid homeostasis in Mycolicibacterium smegmatis. We found that MmbR controls fatty acid β-oxidation and modulates biofilm formation in Mycolicibacterium smegmatis. Although MmbR possesses the properties of nucleoid-associated proteins, it acts as a TetR-like transcription factor, directly regulating and intensively repressing the expression of a group of core genes involved in fatty acid β-oxidation. Furthermore, both long-chain acyl-Coenzyme A and fatty acids appear to regulate the signal molecules modulated by MmbR. The deletion of mmbR led to a significant reduction in intracellular fatty acid content and a decrease in the relative lipid composition of the biofilm. The lack of mmbR led to morphological changes in the mycobacterial colony, defects in biofilm formation and enhanced sensitivity to anti-tuberculosis drugs. Our study is the first to establish a link between the transcriptional regulation of fatty acid β-oxidation genes and lipid homeostasis in mycobacteria.
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Affiliation(s)
- Hui Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhi Su
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yimin Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zheng-Guo He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
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18
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Shao X, Xie Y, Zhang Y, Liu J, Ding Y, Wu M, Wang X, Deng X. Novel therapeutic strategies for treating Pseudomonas aeruginosa infection. Expert Opin Drug Discov 2020; 15:1403-1423. [PMID: 32880507 DOI: 10.1080/17460441.2020.1803274] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Persistent infections caused by the superbug Pseudomonas aeruginosa and its resistance to multiple antimicrobial agents are huge threats to patients with cystic fibrosis as well as those with compromised immune systems. Multidrug-resistant P. aeruginosa has posed a major challenge to conventional antibiotics and therapeutic approaches, which show limited efficacy and cause serious side effects. The public demand for new antibiotics is enormous; yet, drug development pipelines have started to run dry with limited targets available for inventing new antibacterial drugs. Consequently, it is important to uncover potential therapeutic targets. AREAS COVERED The authors review the current state of drug development strategies that are promising in terms of the development of novel and potent drugs to treat P. aeruginosa infection. EXPERT OPINION The prevention of P. aeruginosa infection is increasingly challenging. Furthermore, targeting key virulence regulators has great potential for developing novel anti-P. aeruginosa drugs. Additional promising strategies include bacteriophage therapy, immunotherapies, and antimicrobial peptides. Additionally, the authors believe that in the coming years, the overall network of molecular regulatory mechanism of P. aeruginosa virulence will be fully elucidated, which will provide more novel and promising drug targets for treating P. aeruginosa infections.
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Affiliation(s)
- Xiaolong Shao
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yingpeng Xie
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yingchao Zhang
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Jingui Liu
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yiqing Ding
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota , Grand Forks, North Dakota, USA
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China.,Shenzhen Research Institute, City University of Hong Kong , Shenzhen, China
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19
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Yang S, Xi D, Wang X, Li Y, Li Y, Yan J, Cao B. Vibrio cholerae VC1741 (PsrA) enhances the colonization of the pathogen in infant mice intestines in the presence of the long-chain fatty acid, oleic acid. Microb Pathog 2020; 147:104443. [PMID: 32777352 DOI: 10.1016/j.micpath.2020.104443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/08/2023]
Abstract
Vibrio cholerae is a natural inhabitant of aquatic environments and causes the epidemic diarrheal disease known as cholera. Fatty acid metabolism is closely related to the pathogenicity of V. cholerae. The TetR family transcriptional repressor PsrA regulates the β-oxidation pathway in Pseudomonas aeruginosa; however, little is known about its regulation in V. cholerae. In this study, qRT-PCR revealed that the expression of vc1741 (psrA) increased 40-fold in the small intestines of infant mice compared with that grown in LB medium. The Δvc1741 mutant showed a significant defected in the ability to colonize the small intestines of infant mice with a competitive index (CI) of 0.53. EMSAs indicated that VC1741 could directly bind to the promoter regions of vc1741-fadE1, fadBA, and fadIJ operons, and these bindings were reversed upon addition of the long-chain fatty acid (LCFA), oleic acid. The expression levels of the fadB, fadA, fadI, and fadJ genes were all elevated by approximately 2-fold in the Δvc1741 mutant strain compared with that in the wild-type strain in LB medium, indicating that VC1741 is a repressor for these genes involved in fatty acid degradation. Moreover, ΔfadBA, ΔfadB, and ΔfadA isogenic mutants showed defective abilities to colonize the small intestines of infant mice, with CI values of 0.64, 0.73, and 0.74, respectively. These data provided a mechanistic model in which LCFAs affect the expression of VC1741 to control fatty acid degradation and virulence in V. cholerae.
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Affiliation(s)
- Shuang Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Daoyi Xi
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Xiaochen Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Yuehua Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Yujia Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Junxiang Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Boyang Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China.
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20
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Role of acyl-CoA dehydrogenases from Shewanella livingstonensis Ac10 in docosahexaenoic acid conversion. Biochem Biophys Res Commun 2020; 528:453-458. [DOI: 10.1016/j.bbrc.2020.05.185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/25/2020] [Indexed: 11/21/2022]
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21
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Hierarchical Transcriptional Control of the LuxR Quorum-Sensing Regulon of Vibrio harveyi. J Bacteriol 2020; 202:JB.00047-20. [PMID: 32366592 DOI: 10.1128/jb.00047-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/30/2020] [Indexed: 11/20/2022] Open
Abstract
In vibrios, quorum sensing controls hundreds of genes that are required for cell density-specific behaviors including bioluminescence, biofilm formation, competence, secretion, and swarming motility. The central transcription factor in the quorum-sensing pathway is LuxR/HapR, which directly regulates ∼100 genes in the >400-gene regulon of Vibrio harveyi Among these directly controlled genes are 15 transcription factors, which we predicted would comprise the second tier in the hierarchy of the LuxR regulon. We confirmed that LuxR binds to the promoters of these genes in vitro and quantified the extent of LuxR activation or repression of transcript levels. Transcriptome sequencing (RNA-seq) indicates that most of these transcriptional regulators control only a few genes, with the exception of MetJ, which is a global regulator. The genes regulated by these transcription factors are predicted to be involved in methionine and thiamine biosynthesis, membrane stability, RNA processing, c-di-GMP degradation, sugar transport, and other cellular processes. These data support a hierarchical model in which LuxR directly regulates 15 transcription factors that drive the second level of the gene expression cascade to influence cell density-dependent metabolic states and behaviors in V. harveyi IMPORTANCE Quorum sensing is important for survival of bacteria in nature and influences the actions of bacterial groups. In the relatively few studied examples of quorum-sensing-controlled genes, these genes are associated with competition or cooperation in complex microbial communities and/or virulence in a host. However, quorum sensing in vibrios controls the expression of hundreds of genes, and their functions are mostly unknown or uncharacterized. In this study, we identify the regulators of the second tier of gene expression in the quorum-sensing system of the aquaculture pathogen Vibrio harveyi Our identification of regulatory networks and metabolic pathways controlled by quorum sensing can be extended and compared to other Vibrio species to understand the physiology, ecology, and pathogenesis of these organisms.
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22
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Pan X, Fan Z, Chen L, Liu C, Bai F, Wei Y, Tian Z, Dong Y, Shi J, Chen H, Jin Y, Cheng Z, Jin S, Lin J, Wu W. PvrA is a novel regulator that contributes to Pseudomonas aeruginosa pathogenesis by controlling bacterial utilization of long chain fatty acids. Nucleic Acids Res 2020; 48:5967-5985. [PMID: 32406921 PMCID: PMC7293031 DOI: 10.1093/nar/gkaa377] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 12/19/2022] Open
Abstract
During infection of a host, Pseudomonas aeruginosa orchestrates global gene expression to adapt to the host environment and counter the immune attacks. P. aeruginosa harbours hundreds of regulatory genes that play essential roles in controlling gene expression. However, their contributions to the bacterial pathogenesis remain largely unknown. In this study, we analysed the transcriptomic profile of P. aeruginosa cells isolated from lungs of infected mice and examined the roles of upregulated regulatory genes in bacterial virulence. Mutation of a novel regulatory gene pvrA (PA2957) attenuated the bacterial virulence in an acute pneumonia model. Chromatin immunoprecipitation (ChIP)-Seq and genetic analyses revealed that PvrA directly regulates genes involved in phosphatidylcholine utilization and fatty acid catabolism. Mutation of the pvrA resulted in defective bacterial growth when phosphatidylcholine or palmitic acid was used as the sole carbon source. We further demonstrated that palmitoyl coenzyme A is a ligand for the PvrA, enhancing the binding affinity of PvrA to its target promoters. An arginine residue at position 136 was found to be essential for PvrA to bind palmitoyl coenzyme A. Overall, our results revealed a novel regulatory pathway that controls genes involved in phosphatidylcholine and fatty acid utilization and contributes to the bacterial virulence.
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Affiliation(s)
- Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zheng Fan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lei Chen
- Department of Plant Biology and Ecology, College of Life Science Nankai University, Tianjin 300071 China
| | - Chang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yu Wei
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Zhenyang Tian
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuanyuan Dong
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jing Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hao Chen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shouguang Jin
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
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23
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Velázquez-Sánchez C, Espín G, Peña C, Segura D. The Modification of Regulatory Circuits Involved in the Control of Polyhydroxyalkanoates Metabolism to Improve Their Production. Front Bioeng Biotechnol 2020; 8:386. [PMID: 32426348 PMCID: PMC7204398 DOI: 10.3389/fbioe.2020.00386] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/07/2020] [Indexed: 11/13/2022] Open
Abstract
Poly-(3-hydroxyalkanoates) (PHAs) are bacterial carbon and energy storage compounds. These polymers are synthesized under conditions of nutritional imbalance, where a nutrient is growth-limiting while there is still enough carbon source in the medium. On the other side, the accumulated polymer is mobilized under conditions of nutrient accessibility or by limitation of the carbon source. Thus, it is well known that the accumulation of PHAs is affected by the availability of nutritional resources and this knowledge has been used to establish culture conditions favoring high productivities. In addition to this effect of the metabolic status on PHAs accumulation, several genetic regulatory networks have been shown to drive PHAs metabolism, so the expression of the PHAs genes is under the influence of global or specific regulators. These regulators are thought to coordinate PHAs synthesis and mobilization with the rest of bacterial physiology. While the metabolic and biochemical knowledge related to the biosynthesis of these polymers has led to the development of processes in bioreactors for high-level production and also to the establishment of strategies for metabolic engineering for the synthesis of modified biopolymers, the use of knowledge related to the regulatory circuits controlling PHAs metabolism for strain improvement is scarce. A better understanding of the genetic control systems involved could serve as the foundation for new strategies for strain modification in order to increase PHAs production or to adjust the chemical structure of these biopolymers. In this review, the regulatory systems involved in the control of PHAs metabolism are examined, with emphasis on those acting at the level of expression of the enzymes involved and their potential modification for strain improvement, both for higher titers, or manipulation of polymer properties. The case of the PHAs producer Azotobacter vinelandii is taken as an example of the complexity and variety of systems controlling the accumulation of these interesting polymers in response to diverse situations, many of which could be engineered to improve PHAs production.
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Affiliation(s)
- Claudia Velázquez-Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos Peña
- Departamento Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Daniel Segura
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa. Nat Commun 2019; 10:2931. [PMID: 31270321 PMCID: PMC6610081 DOI: 10.1038/s41467-019-10778-w] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 05/30/2019] [Indexed: 01/12/2023] Open
Abstract
The virulence of Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is regulated by many transcriptional factors (TFs) that control the expression of quorum sensing and protein secretion systems. Here, we report a genome-wide, network-based approach to dissect the crosstalk between 20 key virulence-related TFs. Using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), as well as RNA-seq, we identify 1200 TF-bound genes and 4775 differentially expressed genes. We experimentally validate 347 of these genes as functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that we call ‘Pseudomonas aeruginosa genomic regulatory network’ (PAGnet). Analysis of the network led to the identification of novel functions for two TFs (ExsA and GacA) in quorum sensing and nitrogen metabolism. Furthermore, we present an online platform and R package based on PAGnet to facilitate updating and user-customised analyses. The virulence of Pseudomonas aeruginosa is regulated by many transcriptional factors (TFs). Here, the authors study the crosstalk between 20 key virulence-related TFs, validate 347 functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that is available as an online platform.
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Teper D, Zhang Y, Wang N. TfmR, a novel TetR-family transcriptional regulator, modulates the virulence of Xanthomonas citri in response to fatty acids. MOLECULAR PLANT PATHOLOGY 2019; 20:701-715. [PMID: 30919570 PMCID: PMC6637906 DOI: 10.1111/mpp.12786] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The type III secretion system (T3SS) is required for Xanthomonas citri subsp. citri (Xcc) virulence by translocating effectors into host cytoplasm to promote disease development. The T3SS is controlled by the master transcriptional regulators HrpG and HrpX. While the function of HrpG and HrpX are well characterized, their upstream regulation remains elusive. By using transposon mutagenesis, we identified XAC3052, a TetR-family transcriptional regulator, which regulates T3SS gene expression. Deletion of XAC3052 caused significant reduction in the expression of T3SS and effector genes in vitro and in planta; as well as reduction of virulence in sweet orange (Citrus sinensis). Overexpression of hrpG restored the virulence of ∆XAC3052, suggesting that the loss of virulence is caused by reduction of T3SS gene expression. XAC3052 directly binds to the promoter region and represses the transcription of fadE, mhpC and fadH genes. FadE, MhpC and FadH are not involved in T3SS regulation, but involved in fatty acid catabolism. ∆XAC3052 displays altered fatty acid composition and retarded growth in environments limited in fatty acids. Exogenously supplemented long-chain fatty acids activate the fadE/mhpC promoter and suppress T3SS promoters in wild-type Xac but not in ∆XAC3052. Moreover, the binding of XAC3052 to its target promoter was disrupted by long-chain fatty acids in vitro. Herein, XAC3052 is designated as TfmR (T3SS and Fatty acid Mechanism Regulator). This study identifies a novel regulator of fatty acid metabolism and suggests that fatty acids play an important role in the metabolic control of virulence in Xcc.
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Affiliation(s)
- Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural SciencesUniversity of Florida700 Experiment Station RoadLake Alfred33850USA
| | - Yanan Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural SciencesUniversity of Florida700 Experiment Station RoadLake Alfred33850USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural SciencesUniversity of Florida700 Experiment Station RoadLake Alfred33850USA
- China-USA Citrus Huanglongbing Joint Laboratory (A joint laboratory of The University of Florida’s Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research CenterGannan Normal UniversityGanzhou341000JiangxiChina
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Novovic KD, Malesevic MJ, Filipic BV, Mirkovic NL, Miljkovic MS, Kojic MO, Jovčić BU. PsrA Regulator Connects Cell Physiology and Class 1 Integron Integrase Gene Expression Through the Regulation of lexA Gene Expression in Pseudomonas spp. Curr Microbiol 2019; 76:320-328. [DOI: 10.1007/s00284-019-01626-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/10/2019] [Indexed: 12/30/2022]
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Two Regulators, PA3898 and PA2100, Modulate the Pseudomonas aeruginosa Multidrug Resistance MexAB-OprM and EmrAB Efflux Pumps and Biofilm Formation. Antimicrob Agents Chemother 2018; 62:AAC.01459-18. [PMID: 30297364 DOI: 10.1128/aac.01459-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/29/2018] [Indexed: 11/20/2022] Open
Abstract
It is generally believed that the Pseudomonas aeruginosa biofilm matrix itself acts as a molecular sieve or sink that contributes to significant levels of drug resistance, but it is becoming more apparent that multidrug efflux pumps induced during biofilm growth significantly enhance resistance levels. We present here a novel transcriptional regulator, PA3898, which controls biofilm formation and multidrug efflux pumps in P. aeruginosa A mutant of this regulator significantly reduced the ability of P. aeruginosa to produce biofilm in vitro and affected its in vivo fitness and pathogenesis in Drosophila melanogaster and BALB/c mouse lung infection models. Transcriptome analysis revealed that PA3898 modulates essential virulence genes/pathways, including multidrug efflux pumps and phenazine biosynthesis. Chromatin immunoprecipitation sequencing (ChIP-seq) identified its DNA binding sequences and confirmed that PA3898 directly interacts with promoter regions of four genes/operons, two of which are mexAB-oprM and phz2 Coimmunoprecipitation revealed a regulatory partner of PA3898 as PA2100, and both are required for binding to DNA in electrophoretic mobility shift assays. PA3898 and PA2100 were given the names MdrR1 and MdrR2, respectively, as novel repressors of the mexAB-oprM multidrug efflux operon and activators for another multidrug efflux pump, EmrAB. The interaction between MdrR1 and MdrR2 at the promoter regions of their regulons was further characterized via localized surface plasmon resonance and DNA footprinting. These regulators directly repress the mexAB-oprM operon, independent of its well-established MexR regulator. Mutants of mdrR1 and mdrR2 caused increased resistance to multiple antibiotics in P. aeruginosa, validating the significance of these newly discovered regulators.
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Kumar SS, Tandberg JI, Penesyan A, Elbourne LDH, Suarez-Bosche N, Don E, Skadberg E, Fenaroli F, Cole N, Winther-Larsen HC, Paulsen IT. Dual Transcriptomics of Host-Pathogen Interaction of Cystic Fibrosis Isolate Pseudomonas aeruginosa PASS1 With Zebrafish. Front Cell Infect Microbiol 2018; 8:406. [PMID: 30524971 PMCID: PMC6262203 DOI: 10.3389/fcimb.2018.00406] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/29/2018] [Indexed: 01/09/2023] Open
Abstract
Pseudomonas aeruginosa is a significant cause of mortality in patients with cystic fibrosis (CF). To explore the interaction of the CF isolate P. aeruginosa PASS1 with the innate immune response, we have used Danio rerio (zebrafish) as an infection model. Confocal laser scanning microscopy (CLSM) enabled visualization of direct interactions between zebrafish macrophages and P. aeruginosa PASS1. Dual RNA-sequencing of host-pathogen was undertaken to profile RNA expression simultaneously in the pathogen and the host during P. aeruginosa infection. Following establishment of infection in zebrafish embryos with PASS1, 3 days post infection (dpi), there were 6739 genes found to be significantly differentially expressed in zebrafish and 176 genes in PASS1. A range of virulence genes were upregulated in PASS1, including genes encoding pyoverdine biosynthesis, flagellin, non-hemolytic phospholipase C, proteases, superoxide dismutase and fimbrial subunits. Additionally, iron and phosphate acquisition genes were upregulated in PASS1 cells in the zebrafish. Transcriptional changes in the host immune response genes highlighted phagocytosis as a key response mechanism to PASS1 infection. Transcriptional regulators of neutrophil and macrophage phagocytosis were upregulated alongside transcriptional regulators governing response to tissue injury, infection, and inflammation. The zebrafish host showed significant downregulation of the ribosomal RNAs and other genes involved in translation, suggesting that protein translation in the host is affected by PASS1 infection.
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Affiliation(s)
- Sheemal S Kumar
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Julia I Tandberg
- Department of Pharmaceutical Biosciences, Centre of Integrative Microbial Evolution, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Anahit Penesyan
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Liam D H Elbourne
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Nadia Suarez-Bosche
- Microscopy Unit, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Emily Don
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Eline Skadberg
- Department of Pharmaceutical Biosciences, Centre of Integrative Microbial Evolution, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Federico Fenaroli
- Department of Biosciences, The Faculty of Mathematic and Natural Sciences, University of Oslo, Oslo, Norway
| | - Nicholas Cole
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Hanne Cecilie Winther-Larsen
- Department of Pharmaceutical Biosciences, Centre of Integrative Microbial Evolution, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Ian T Paulsen
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
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29
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Baker LY, Hobby CR, Siv AW, Bible WC, Glennon MS, Anderson DM, Symes SJ, Giles DK. Pseudomonas aeruginosa responds to exogenous polyunsaturated fatty acids (PUFAs) by modifying phospholipid composition, membrane permeability, and phenotypes associated with virulence. BMC Microbiol 2018; 18:117. [PMID: 30217149 PMCID: PMC6137939 DOI: 10.1186/s12866-018-1259-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 09/05/2018] [Indexed: 12/20/2022] Open
Abstract
Background Pseudomonas aeruginosa, a common opportunistic pathogen, is known to cause infections in a variety of compromised human tissues. An emerging mechanism for microbial survival is the incorporation of exogenous fatty acids to alter the cell’s membrane phospholipid profile. With these findings, we show that exogenous fatty acid exposure leads to changes in bacterial membrane phospholipid structure, membrane permeability, virulence phenotypes and consequent stress responses that may influence survival and persistence of Pseudomonas aeruginosa. Results Thin-layer chromatography and ultra performance liquid chromatography / ESI-mass spectrometry indicated alteration of bacterial phospholipid profiles following growth in the presence of polyunsaturated fatty acids (PUFAs) (ranging in carbon length and unsaturation). The exogenously supplied fatty acids were incorporated into the major bacterial phospholipids phosphatidylethanolamine and phosphatidylglycerol. The incorporation of fatty acids increased membrane permeability as judged by both accumulation and exclusion of ethidium bromide. Individual fatty acids were identified as modifying resistance to the cyclic peptide antibiotics polymyxin B and colistin, but not the beta-lactam imipenem. Biofilm formation was increased by several PUFAs and significant fluctuations in swimming motility were observed. Conclusions Our results emphasize the relevance and complexity of exogenous fatty acids in the membrane physiology and pathobiology of a medically important pathogen. P. aeruginosa exhibits versatility with regard to utilization of and response to exogenous fatty acids, perhaps revealing potential strategies for prevention and control of infection. Electronic supplementary material The online version of this article (10.1186/s12866-018-1259-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lyssa Y Baker
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Chelsea R Hobby
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Andrew W Siv
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - William C Bible
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Michael S Glennon
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Derek M Anderson
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Steven J Symes
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - David K Giles
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA.
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30
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Wang J, Yu H, Zhu K. Employing metabolic engineered lipolytic microbial platform for 1-alkene one-step conversion. BIORESOURCE TECHNOLOGY 2018; 263:172-179. [PMID: 29738980 DOI: 10.1016/j.biortech.2018.04.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/29/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
1-Alkenes are traditionally used as basic chemicals with great importance. Biosynthetic 1-alkenes also have the potential to serve as biofuels. In this study, we engineered a Pseudomonas lipolytic microbial platform for 1-alkene production using hydrophobic substrate as sole carbon source. Fatty acid decarboxylase UndA and UndB were cloned and expressed, which successfully produced 1-alkenes. Optimal culturing temperature and the interruption of competitive pathway were proven to be beneficial to 1-alkene synthesis. Chromosomal integration of UndB conferred 177.8 mg/L 1-alkenes (mainly 1-undecene) in lauric acid medium and 128.9 mg/L 1-alkenes (mainly 1-pentadecene) in palm oil medium. Thioesterase expression, adjustments of fatty acid degradation pathway and a second copy of UndB improved 1-alkene titer to 1102.6 mg/L using lauric acid and 778.4 mg/L using palm oil. All in all, this study offers the first demonstration of lipolytic microbial 1-alkene producing platform with highest reported 1-alkene product titer up to date.
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Affiliation(s)
- Juli Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiying Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kun Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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31
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Heacock-Kang Y, Zarzycki-Siek J, Sun Z, Poonsuk K, Bluhm AP, Cabanas D, Fogen D, McMillan IA, Chuanchuen R, Hoang TT. Novel dual regulators of Pseudomonas aeruginosa essential for productive biofilms and virulence. Mol Microbiol 2018; 109:401-414. [PMID: 29995308 PMCID: PMC6158065 DOI: 10.1111/mmi.14063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 01/14/2023]
Abstract
Gene regulation network in Pseudomonas aeruginosa is complex. With a relatively large genome (6.2 Mb), there is a significant portion of genes that are proven or predicted to be transcriptional regulators. Many of these regulators have been shown to play important roles in biofilm formation and maintenance. In this study, we present a novel transcriptional regulator, PA1226, which modulates biofilm formation and virulence in P. aeruginosa. Mutation in the gene encoding this regulator abolished the ability of P. aeruginosa to produce biofilms in vitro, without any effect on the planktonic growth. This regulator is also essential for the in vivo fitness and pathogenesis in both Drosophila melanogaster and BALB/c mouse lung infection models. Transcriptome analysis revealed that PA1226 regulates many essential virulence genes/pathways, including those involved in alginate, pili, and LPS biosynthesis. Genes/operons directly regulated by PA1226 and potential binding sequences were identified via ChIP-seq. Attempts to confirm the binding sequences by electrophoretic mobility shift assay led to the discovery of a co-regulator, PA1413, via co-immunoprecipitation assay. PA1226 and PA1413 were shown to bind collaboratively to the promoter regions of their regulons. A model is proposed, summarizing our finding on this novel dual-regulation system.
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Affiliation(s)
- Yun Heacock-Kang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Jan Zarzycki-Siek
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Zhenxin Sun
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Kanchana Poonsuk
- Department of Veterinary Public Health, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Andrew P Bluhm
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Darlene Cabanas
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Dawson Fogen
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Ian A McMillan
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Rungtip Chuanchuen
- Department of Veterinary Public Health, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tung T Hoang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
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Carbon flux to growth or polyhydroxyalkanoate synthesis under microaerophilic conditions is affected by fatty acid chain-length in Pseudomonas putida LS46. Appl Microbiol Biotechnol 2018; 102:6437-6449. [PMID: 29799090 DOI: 10.1007/s00253-018-9055-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/26/2018] [Indexed: 12/21/2022]
Abstract
Economical production of medium-chain length polyhydroxyalkanoates (mcl-PHA) is dependent on efficient cultivation processes. This work describes growth and mcl-PHA synthesis characteristics of Pseudomonas putida LS46 when grown on medium-chain length fatty acids (octanoic acid) and lower-cost long-chain fatty acids (LCFAs, derived from hydrolyzed canola oil) in microaerophilic environments. Growth on octanoic acid ceased when the oxygen uptake rate was limited by the oxygen transfer rate, and mcl-PHA accumulated to 61.9% of the cell dry mass. From LCFAs, production of non-PHA cell mass continued at a rate of 0.36 g L-1 h-1 under oxygen-limited conditions, while mcl-PHA accumulated simultaneously to 31% of the cell dry mass. The titer of non-PHA cell mass from LCFAs at 14 h post-inoculation was double that obtained from octanoic acid in bioreactors operated with identical feeding and aeration conditions. While the productivity for octanoic acid was higher by 14 h, prolonged cultivation on LCFAs achieved similar productivity but with twice the PHA titer. Simultaneous co-feeding of each substrate demonstrated the continued cell growth under microaerophilic conditions characteristic of LCFAs, and the resulting polymer was dominant in C8 monomers. Furthermore, co-feeding resulted in improved PHA titer and volumetric productivity compared to either substrate individually. These results suggest that LCFAs improve growth of P. putida in oxygen-limited environments and could reduce production costs since more non-PHA cell mass, the cellular factories required to produce mcl-PHA and the most oxygen-intensive cellular process, can be produced for a given oxygen transfer rate.
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Meadows JA, Willsey GG, Wargo MJ. Differential requirements for processing and transport of short-chain versus long-chain O-acylcarnitines in Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2018; 164:635-645. [PMID: 29517479 PMCID: PMC5982139 DOI: 10.1099/mic.0.000638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/19/2018] [Indexed: 11/18/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa can metabolize carnitine and O-acylcarnitines, which are abundant in host muscle and other tissues. Acylcarnitines are metabolized to carnitine and a fatty acid. The liberated carnitine and its catabolic product, glycine betaine, can be used as osmoprotectants, to induce the secreted phospholipase C PlcH, and as sole carbon, nitrogen and energy sources. P. aeruginosa is incapable of de novo synthesis of carnitine and acylcarnitines, therefore they must be imported from an exogenous source. In this study, we present the first characterization of bacterial acylcarnitine transport. Short-chain acylcarnitines are imported by the ABC transporter CaiX-CbcWV. Medium- and long-chain acylcarnitines (MCACs and LCACs) are hydrolysed extracytoplasmically and the free carnitine is transported primarily through CaiX-CbcWV. These findings suggest that the periplasmic protein CaiX has a binding pocket that permits short acyl chains on its carnitine ligand and that there are one or more secreted hydrolases that cleave MCACs and LCACs. To identify the secreted hydrolase(s), we used a saturating genetic screen and transcriptomics followed by phenotypic analyses, but neither led to identification of a contributing hydrolase, supporting but not conclusively demonstrating redundancy for this activity.
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Affiliation(s)
- Jamie A. Meadows
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Graham G. Willsey
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Matthew J. Wargo
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
- The Vermont Lung Center, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
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Wells G, Palethorpe S, Pesci EC. PsrA controls the synthesis of the Pseudomonas aeruginosa quinolone signal via repression of the FadE homolog, PA0506. PLoS One 2017; 12:e0189331. [PMID: 29220387 PMCID: PMC5722320 DOI: 10.1371/journal.pone.0189331] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/22/2017] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous, Gram-negative opportunistic pathogen that can cause disease in various sites within the human body. This bacterium is a major source of nosocomial infections that are often difficult to treat due to high intrinsic antibiotic resistance and coordinated virulence factor production. P. aeruginosa utilizes three cell-to-cell signaling systems to regulate numerous genes in response to cell density. One of these systems utilizes the small molecule 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas quinolone signal [PQS]) as a signal that acts as a co-inducer for the transcriptional regulator PqsR. Quinolone signaling is required for virulence in multiple infection models, and PQS is produced during human infections, making this system an attractive target for potential drug development. In this study we have examined the role of a TetR-type transcriptional regulator, PsrA, in the regulation of PQS production by P. aeruginosa. Previous studies showed that PsrA regulates genes of the fatty acid β-oxidation pathway, including PA0506, which encodes a FadE homolog. In this report, we show that deletion of psrA resulted in a large decrease in PQS production and that co-deletion of PA0506 allowed PQS production to be restored to a wild type level. We also found that PQS production could be restored to the psrA mutant by the addition of oleic or octanoic acid. Taken together, our data suggest that psrA positively affects PQS production by repressing the transcription of PA0506, which leads to a decrease in the conversion of acyl-CoA compounds to enoyl-CoA compounds, thereby allowing some octanoyl-CoA to escape the ß-oxidation pathway and serve as a PQS precursor.
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Affiliation(s)
- Greg Wells
- Department of Microbiology and Immunology, The Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
| | - Samantha Palethorpe
- Department of Microbiology and Immunology, The Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
| | - Everett C. Pesci
- Department of Microbiology and Immunology, The Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
- * E-mail:
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Exogenous Polyunsaturated Fatty Acids Impact Membrane Remodeling and Affect Virulence Phenotypes among Pathogenic Vibrio Species. Appl Environ Microbiol 2017; 83:AEM.01415-17. [PMID: 28864654 DOI: 10.1128/aem.01415-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/25/2017] [Indexed: 01/24/2023] Open
Abstract
The pathogenic Vibrio species (V. cholerae, V. parahaemolyticus, and V. vulnificus) represent a constant threat to human health, causing foodborne and skin wound infections as a result of ingestion of or exposure to contaminated water and seafood. Recent studies have highlighted Vibrio's ability to acquire fatty acids from environmental sources and assimilate them into cell membranes. The possession and conservation of such machinery provokes consideration of fatty acids as important factors in the pathogenic lifestyle of Vibrio species. The findings here link exogenous fatty acid exposure to changes in bacterial membrane phospholipid structure, permeability, phenotypes associated with virulence, and consequent stress responses that may impact survival and persistence of pathogenic Vibrio species. Polyunsaturated fatty acids (PUFAs) (ranging in carbon length and unsaturation) supplied in growth medium were assimilated into bacterial phospholipids, as determined by thin-layer chromatography and liquid chromatography-mass spectrometry. The incorporation of fatty acids variably affected membrane permeability, as judged by uptake of the hydrophobic compound crystal violet. For each species, certain fatty acids were identified as affecting resistance to antimicrobial peptide treatment. Significant fluctuations were observed with regard to both motility and biofilm formation following growth in the presence of individual PUFAs. Our results illustrate the important and complex roles of exogenous fatty acids in the membrane physiology and virulence of a bacterial genus that inhabits aquatic and host environments containing an abundance of diverse fatty acids.IMPORTANCE Bacterial responses to fatty acids include, but are not limited to, degradation for metabolic gain, modification of membrane lipids, alteration of protein function, and regulation of gene expression. Vibrio species exhibit significant diversity with regard to the machinery known to participate in the uptake and incorporation of fatty acids into their membranes. Both aquatic and host niches occupied by Vibrio are rife with various free fatty acids and fatty acid-containing lipids. The roles of fatty acids in the environmental survival and pathogenesis of bacteria have begun to emerge and are expected to expand significantly. The current study demonstrates the responsiveness of V. cholerae, V. parahaemolyticus, and V. vulnificus to exogenous PUFAs. In addition to phospholipid remodeling, PUFA assimilation impacts membrane permeability, motility, biofilm formation, and resistance to polymyxin B.
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Turcano L, Visaggio D, Frangipani E, Missineo A, Andreini M, Altamura S, Visca P, Bresciani A. Identification by High-Throughput Screening of Pseudomonas Acyl-Coenzyme A Synthetase Inhibitors. SLAS DISCOVERY 2017; 22:897-905. [PMID: 28346095 DOI: 10.1177/2472555216689283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Pseudomonas infections are common among hospitalized, immunocompromised, and chronic lung disease patients. These infections are recalcitrant to common antibacterial therapies due to inherent antibiotic resistance. To meet the need of new anti- Pseudomonas drugs, a sensitive, homogenous, and robust assay was developed with the aim of identifying inhibitors of acyl-coenzyme A synthetases (ACSs) from Pseudomonas. Given the importance of fatty acids for in vivo nutrition of Pseudomonas, such inhibitors might have the potential to reduce the bacterial fitness during infection. The assay, based on a coupled reaction between the Pseudomonas spp. ACS and the firefly luciferase, allowed the identification of three classes of inhibitors by screening of a diverse compound collection. These compounds were confirmed to reversibly bind ACS with potencies in the micromolar range. Two classes were found to compete with acyl-coenzyme A, while the third one was competitive with fatty acid binding. Although these compounds inhibit the bacterial ACS in cell-free assays, they show modest or no effect on Pseudomonas growth in vitro.
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Affiliation(s)
| | | | | | | | | | | | - Paolo Visca
- 2 Department of Science, RomaTre University, Rome, Italy
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Woo TE, Duong J, Jervis NM, Rabin HR, Parkins MD, Storey DG. Virulence adaptations of Pseudomonas aeruginosa isolated from patients with non-cystic fibrosis bronchiectasis. MICROBIOLOGY-SGM 2016; 162:2126-2135. [PMID: 27902425 DOI: 10.1099/mic.0.000393] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pseudomonas aeruginosa is a major pathogen in chronic lung diseases such as cystic fibrosis (CF) and non-cystic fibrosis bronchiectasis (nCFB). Much of our understanding regarding infections in nCFB patients is extrapolated from findings in CF with little direct investigation on the adaptation of P. aeruginosa in nCFB patients. As such, we investigated whether the adaptation of P. aeruginosa was indeed similar between nCFB and CF. From our prospectively collected biobank, we identified 40 nCFB patients who had repeated P. aeruginosa isolates separated by ≥6 months and compared these to a control population of 28 CF patients. A total of 84 nCFB isolates [40 early (defined as the earliest isolate in the biobank) and 41 late (defined as the last available isolate in the biobank)] were compared to 83 CF isolates (39 early and 44 late). We assessed the isolates for protease, lipase and elastase production; mucoid phenotype; swarm and swim motility; biofilm production; and the presence of the lasR mutant phenotype. Overall, we observed phenotypic heterogeneity in both nCFB and CF isolates and found that P. aeruginosa adapted to the nCFB lung environment similarly to the way observed in CF isolates in terms of protease and elastase expression, motility and biofilm formation. However, significant differences between nCFB and CF isolates were observed in lipase expression, which may allude to distinct characteristics found in the lung environment of nCFB patients. We also sought to determine virulence potential over time in nCFB P. aeruginosa isolates and found that virulence decreased over time, similar to CF.
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Affiliation(s)
- Taylor E Woo
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Jessica Duong
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Nicole M Jervis
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Harvey R Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.,Department of Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.,Department of Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Douglas G Storey
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.,Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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Sana TG, Berni B, Bleves S. The T6SSs of Pseudomonas aeruginosa Strain PAO1 and Their Effectors: Beyond Bacterial-Cell Targeting. Front Cell Infect Microbiol 2016; 6:61. [PMID: 27376031 PMCID: PMC4899435 DOI: 10.3389/fcimb.2016.00061] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/23/2016] [Indexed: 02/05/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen responsible for many diseases such as chronic lung colonization in cystic fibrosis patients and acute infections in hospitals. The capacity of P. aeruginosa to be pathogenic toward several hosts is notably due to different secretion systems. Amongst them, P. aeruginosa encodes three Type Six Secretion Systems (T6SS), named H1- to H3-T6SS, that act against either prokaryotes and/or eukaryotic cells. They are independent from each other and inject diverse toxins that interact with different components in the host cell. Here we summarize the roles of these T6SSs in the PAO1 strain, as well as the toxins injected and their targets. While H1-T6SS is only involved in antiprokaryotic activity through at least seven different toxins, H2-T6SS and H3-T6SS are also able to target prokaryotic as well as eukaryotic cells. Moreover, recent studies proposed that H2- and H3-T6SS have a role in epithelial cells invasion by injecting at least three different toxins. The diversity of T6SS effectors is astounding and other effectors still remain to be discovered. In this review, we present a table with other putative P. aeruginosa strain PAO1 T6SS-dependent effectors. Altogether, the T6SSs of P. aeruginosa are important systems that help fight other bacteria for their ecological niche, and are important in the pathogenicity process.
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Affiliation(s)
- Thibault G Sana
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, Centre National de la Recherche Scientifique and Aix-Marseille UniversityMarseille, France; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford UniversityStanford, CA, USA
| | - Benjamin Berni
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, Centre National de la Recherche Scientifique and Aix-Marseille University Marseille, France
| | - Sophie Bleves
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, Centre National de la Recherche Scientifique and Aix-Marseille University Marseille, France
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Cavaleiro AJ, Pereira MA, Guedes AP, Stams AJM, Alves MM, Sousa DZ. Conversion of Cn-Unsaturated into Cn-2-Saturated LCFA Can Occur Uncoupled from Methanogenesis in Anaerobic Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3082-3090. [PMID: 26810160 DOI: 10.1021/acs.est.5b03204] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Fat, oils, and grease present in complex wastewater can be readily converted to methane, but the energy potential of these compounds is not always recyclable, due to incomplete degradation of long chain fatty acids (LCFA) released during lipids hydrolysis. Oleate (C18:1) is generally the dominant LCFA in lipid-containing wastewater, and its conversion in anaerobic bioreactors results in palmitate (C16:0) accumulation. The reason why oleate is continuously converted to palmitate without further degradation via β-oxidation is still unknown. In this work, the influence of methanogenic activity in the initial conversion steps of unsaturated LCFA was studied in 10 bioreactors continuously operated with saturated or unsaturated C16- and C18-LCFA, in the presence or absence of the methanogenic inhibitor bromoethanesulfonate (BrES). Saturated Cn-2-LCFA accumulated both in the presence and absence of BrES during the degradation of unsaturated Cn-LCFA, and represented more than 50% of total LCFA. In the presence of BrES further conversion of saturated intermediates did not proceed, not even when prolonged batch incubation was applied. As the initial steps of unsaturated LCFA degradation proceed uncoupled from methanogenesis, accumulation of saturated LCFA can be expected. Analysis of the active microbial communities suggests a role for facultative anaerobic bacteria in the initial steps of unsaturated LCFA biodegradation. Understanding this role is now imperative to optimize methane production from LCFA.
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Affiliation(s)
- Ana J Cavaleiro
- Centre of Biological Engineering, University of Minho , Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria Alcina Pereira
- Centre of Biological Engineering, University of Minho , Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana P Guedes
- Centre of Biological Engineering, University of Minho , Campus de Gualtar, 4710-057 Braga, Portugal
| | - Alfons J M Stams
- Centre of Biological Engineering, University of Minho , Campus de Gualtar, 4710-057 Braga, Portugal
- Laboratory of Microbiology, Wageningen University , Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho , Campus de Gualtar, 4710-057 Braga, Portugal
| | - Diana Z Sousa
- Centre of Biological Engineering, University of Minho , Campus de Gualtar, 4710-057 Braga, Portugal
- Laboratory of Microbiology, Wageningen University , Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions. mSystems 2016; 1:mSystems00025-15. [PMID: 27822512 PMCID: PMC5069748 DOI: 10.1128/msystems.00025-15] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 12/21/2022] Open
Abstract
The increasing number of genome-wide assays of gene expression available from public databases presents opportunities for computational methods that facilitate hypothesis generation and biological interpretation of these data. We present an unsupervised machine learning approach, ADAGE (analysis using denoising autoencoders of gene expression), and apply it to the publicly available gene expression data compendium for Pseudomonas aeruginosa. In this approach, the machine-learned ADAGE model contained 50 nodes which we predicted would correspond to gene expression patterns across the gene expression compendium. While no biological knowledge was used during model construction, cooperonic genes had similar weights across nodes, and genes with similar weights across nodes were significantly more likely to share KEGG pathways. By analyzing newly generated and previously published microarray and transcriptome sequencing data, the ADAGE model identified differences between strains, modeled the cellular response to low oxygen, and predicted the involvement of biological processes based on low-level gene expression differences. ADAGE compared favorably with traditional principal component analysis and independent component analysis approaches in its ability to extract validated patterns, and based on our analyses, we propose that these approaches differ in the types of patterns they preferentially identify. We provide the ADAGE model with analysis of all publicly available P. aeruginosa GeneChip experiments and open source code for use with other species and settings. Extraction of consistent patterns across large-scale collections of genomic data using methods like ADAGE provides the opportunity to identify general principles and biologically important patterns in microbial biology. This approach will be particularly useful in less-well-studied microbial species. IMPORTANCE The quantity and breadth of genome-scale data sets that examine RNA expression in diverse bacterial and eukaryotic species are increasing more rapidly than for curated knowledge. Our ADAGE method integrates such data without requiring gene function, gene pathway, or experiment labeling, making practical its application to any large gene expression compendium. We built a Pseudomonas aeruginosa ADAGE model from a diverse set of publicly available experiments without any prespecified biological knowledge, and this model was accurate and predictive. We provide ADAGE results for the complete P. aeruginosa GeneChip compendium for use by researchers studying P. aeruginosa and source code that facilitates ADAGE's application to other species and data types. Author Video: An author video summary of this article is available.
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Acinetobacter baumannii Is Dependent on the Type II Secretion System and Its Substrate LipA for Lipid Utilization and In Vivo Fitness. J Bacteriol 2015; 198:711-9. [PMID: 26668261 DOI: 10.1128/jb.00622-15] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Gram-negative bacteria express a number of sophisticated secretion systems to transport virulence factors across the cell envelope, including the type II secretion (T2S) system. Genes for the T2S components GspC through GspN and PilD are conserved among isolates of Acinetobacter baumannii, an increasingly common nosocomial pathogen that is developing multidrug resistance at an alarming rate. In contrast to most species, however, the T2S genes are dispersed throughout the genome rather than linked into one or two operons. Despite this unique genetic organization, we show here that the A. baumannii T2S system is functional. Deletion of gspD or gspE in A. baumannii ATCC 17978 results in loss of secretion of LipA, a lipase that breaks down long-chain fatty acids. Due to a lack of extracellular lipase, the gspD mutant, the gspE mutant, and a lipA deletion strain are incapable of growth on long-chain fatty acids as a sole source of carbon, while their growth characteristics are indistinguishable from those of the wild-type strain in nutrient-rich broth. Genetic inactivation of the T2S system and its substrate, LipA, also has a negative impact on in vivo fitness in a neutropenic murine model for bacteremia. Both the gspD and lipA mutants are outcompeted by the wild-type strain as judged by their reduced numbers in spleen and liver following intravenous coinoculation. Collectively, our findings suggest that the T2S system plays a hitherto-unrecognized role in in vivo survival of A. baumannii by transporting a lipase that may contribute to fatty acid metabolism. IMPORTANCE Infections by multidrug-resistant Acinetobacter baumannii are a growing health concern worldwide, underscoring the need for a better understanding of the molecular mechanisms by which this pathogen causes disease. In this study, we demonstrated that A. baumannii expresses a functional type II secretion (T2S) system that is responsible for secretion of LipA, an extracellular lipase required for utilization of exogenously added lipids. The T2S system and the secreted lipase support in vivo colonization and thus contribute to the pathogenic potential of A. baumannii.
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Fu J, Sharma P, Spicer V, Krokhin OV, Zhang X, Fristensky B, Cicek N, Sparling R, Levin DB. Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids. PLoS One 2015; 10:e0142322. [PMID: 26544181 PMCID: PMC4636370 DOI: 10.1371/journal.pone.0142322] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/19/2015] [Indexed: 12/19/2022] Open
Abstract
Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. 'Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the 'Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining the monomer composition of mcl-PHA polymers. Understanding the relationships between genome content, gene and gene product expression, and how these factors influence polymer synthesis, will aid in optimization of mcl-PHA production by P. putida LS46 using biodiesel waste streams.
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Affiliation(s)
- Jilagamazhi Fu
- Department of Biosystem Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Parveen Sharma
- Department of Biosystem Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vic Spicer
- Department of Internal Medicine & Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Oleg V. Krokhin
- Department of Internal Medicine & Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Xiangli Zhang
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian Fristensky
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nazim Cicek
- Department of Biosystem Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David. B. Levin
- Department of Biosystem Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
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Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C. A reproducible approach to high-throughput biological data acquisition and integration. PeerJ 2015; 3:e791. [PMID: 26157642 PMCID: PMC4493686 DOI: 10.7717/peerj.791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/04/2015] [Indexed: 12/25/2022] Open
Abstract
Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa.
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Affiliation(s)
- Daniela Börnigen
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yo Sup Moon
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
| | - Gholamali Rahnavard
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Levi Waldron
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA.,City University of New York School of Public Health, Hunter College, New York, NY, USA
| | - Lauren McIver
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
| | - Afrah Shafquat
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Larissa Miropolsky
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
| | | | - Xochitl C Morgan
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S Garrett
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Curtis Huttenhower
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Fonseca P, de la Peña F, Prieto MA. A role for the regulator PsrA in the polyhydroxyalkanoate metabolism of Pseudomonas putida KT2440. Int J Biol Macromol 2014; 71:14-20. [DOI: 10.1016/j.ijbiomac.2014.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/31/2014] [Accepted: 04/05/2014] [Indexed: 10/25/2022]
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Heroven AK, Böhme K, Dersch P. The Csr/Rsm system of Yersinia and related pathogens. RNA Biol 2014; 9:379-91. [DOI: 10.4161/rna.19333] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Jackson AA, Daniels EF, Hammond JH, Willger SD, Hogan DA. Global regulator Anr represses PlcH phospholipase activity in Pseudomonas aeruginosa when oxygen is limiting. MICROBIOLOGY-SGM 2014; 160:2215-2225. [PMID: 25073853 DOI: 10.1099/mic.0.081158-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Haemolytic phospholipase C (PlcH) is a potent virulence and colonization factor that is expressed at high levels by Pseudomonas aeruginosa within the mammalian host. The phosphorylcholine liberated from phosphatidylcholine and sphingomyelin by PlcH is further catabolized into molecules that both support growth and further induce plcH expression. We have shown previously that the catabolism of PlcH-released choline leads to increased activity of Anr, a global transcriptional regulator that promotes biofilm formation and virulence. Here, we demonstrated the presence of a negative feedback loop in which Anr repressed plcH transcription and we proposed that this regulation allowed for PlcH levels to be maintained in a way that promotes productive host-pathogen interactions. Evidence for Anr-mediated regulation of PlcH came from data showing that growth at low oxygen (1%) repressed PlcH abundance and plcH transcription in the WT, and that plcH transcription was enhanced in an Δanr mutant. The plcH promoter featured an Anr consensus sequence that was conserved across all P. aeruginosa genomes and mutation of conserved nucleotides within the Anr consensus sequence increased plcH expression under hypoxic conditions. The Anr-regulated transcription factor Dnr was not required for this effect. The loss of Anr was not sufficient to completely derepress plcH transcription as GbdR, a positive regulator of plcH, was required for expression. Overexpression of Anr was sufficient to repress plcH transcription even at 21 % oxygen. Anr repressed plcH expression and phospholipase C activity in a cell culture model for P. aeruginosa-epithelial cell interactions.
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Affiliation(s)
- Angelyca A Jackson
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 208 Vail Building, Hanover, NH 03755, USA
| | - Emily F Daniels
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 208 Vail Building, Hanover, NH 03755, USA
| | - John H Hammond
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 208 Vail Building, Hanover, NH 03755, USA
| | - Sven D Willger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 208 Vail Building, Hanover, NH 03755, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 208 Vail Building, Hanover, NH 03755, USA
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Sun Z, Kang Y, Norris MH, Troyer RM, Son MS, Schweizer HP, Dow SW, Hoang TT. Blocking phosphatidylcholine utilization in Pseudomonas aeruginosa, via mutagenesis of fatty acid, glycerol and choline degradation pathways, confirms the importance of this nutrient source in vivo. PLoS One 2014; 9:e103778. [PMID: 25068317 PMCID: PMC4113454 DOI: 10.1371/journal.pone.0103778] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/02/2014] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa can grow to very high-cell-density (HCD) during infection of the cystic fibrosis (CF) lung. Phosphatidylcholine (PC), the major component of lung surfactant, has been hypothesized to support HCD growth of P. aeruginosa in vivo. The phosphorylcholine headgroup, a glycerol molecule, and two long-chain fatty acids (FAs) are released by enzymatic cleavage of PC by bacterial phospholipase C and lipases. Three different bacterial pathways, the choline, glycerol, and fatty acid degradation pathways, are then involved in the degradation of these PC components. Here, we identified five potential FA degradation (Fad) related fadBA-operons (fadBA1-5, each encoding 3-hydroxyacyl-CoA dehydrogenase and acyl-CoA thiolase). Through mutagenesis and growth analyses, we showed that three (fadBA145) of the five fadBA-operons are dominant in medium-chain and long-chain Fad. The triple fadBA145 mutant also showed reduced ability to degrade PC in vitro. We have previously shown that by partially blocking Fad, via mutagenesis of fadBA5 and fadDs, we could significantly reduce the ability of P. aeruginosa to replicate on FA and PC in vitro, as well as in the mouse lung. However, no studies have assessed the ability of mutants, defective in choline and/or glycerol degradation in conjunction with Fad, to grow on PC or in vivo. Hence, we constructed additional mutants (ΔfadBA145ΔglpD, ΔfadBA145ΔbetAB, and ΔfadBA145ΔbetABΔglpD) significantly defective in the ability to degrade FA, choline, and glycerol and, therefore, PC. The analysis of these mutants in the BALB/c mouse lung infection model showed significant inability to utilize PC in vitro, resulted in decreased replication fitness and competitiveness in vivo compared to the complement strain, although there was little to no variation in typical virulence factor production (e.g., hemolysin, lipase, and protease levels). This further supports the hypothesis that lung surfactant PC serves as an important nutrient for P. aeruginosa during CF lung infection.
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Affiliation(s)
- Zhenxin Sun
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Yun Kang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Michael H. Norris
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Ryan M. Troyer
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mike S. Son
- Department of Biological Sciences, Plymouth State University, Plymouth, New Hampshire, United States of America
| | - Herbert P. Schweizer
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Steven W. Dow
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Tung T. Hoang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
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48
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Turner KH, Everett J, Trivedi U, Rumbaugh KP, Whiteley M. Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection. PLoS Genet 2014; 10:e1004518. [PMID: 25057820 PMCID: PMC4109851 DOI: 10.1371/journal.pgen.1004518] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/04/2014] [Indexed: 12/29/2022] Open
Abstract
Opportunistic infections caused by Pseudomonas aeruginosa can be acute or chronic. While acute infections often spread rapidly and can cause tissue damage and sepsis with high mortality rates, chronic infections can persist for weeks, months, or years in the face of intensive clinical intervention. Remarkably, this diverse infectious capability is not accompanied by extensive variation in genomic content, suggesting that the genetic capacity to be an acute or a chronic pathogen is present in most P. aeruginosa strains. To investigate the genetic requirements for acute and chronic pathogenesis in P. aeruginosa infections, we combined high-throughput sequencing-mediated transcriptome profiling (RNA-seq) and genome-wide insertion mutant fitness profiling (Tn-seq) to characterize gene expression and fitness determinants in murine models of burn and non-diabetic chronic wound infection. Generally we discovered that expression of a gene in vivo is not correlated with its importance for fitness, with the exception of metabolic genes. By combining metabolic models generated from in vivo gene expression data with mutant fitness profiles, we determined the nutritional requirements for colonization and persistence in these infections. Specifically, we found that long-chain fatty acids represent a major carbon source in both chronic and acute wounds, and P. aeruginosa must biosynthesize purines, several amino acids, and most cofactors during infection. In addition, we determined that P. aeruginosa requires chemotactic flagellar motility for fitness and virulence in acute burn wound infections, but not in non-diabetic chronic wound infections. Our results provide novel insight into the genetic requirements for acute and chronic P. aeruginosa wound infections and demonstrate the power of using both gene expression and fitness profiling for probing bacterial virulence. Soft tissue infections, such as those in burns, bed sores, and diabetic ulcers, are a significant healthcare and economic burden in the developed and developing world. The opportunistic pathogen P. aeruginosa can cause both acute and chronic infections, and the trajectory of these two types of infections is vastly different. We used high-throughput sequencing to profile P. aeruginosa genome-wide gene expression and mutant fitness during mouse model acute and non-diabetic chronic wound infections. Using these data, we show that wounds are nutrient-rich growth environments in which long-chain fatty acids are a primary source of carbon and energy. We also show that the ability to travel along spatio-chemical gradients by chemotaxis is critical for bacterial fitness and virulence in acute but not chronic infections. Our results demonstrate the utility of simultaneous mutant fitness and gene expression profiling to discover critical functions in complex growth environments.
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Affiliation(s)
- Keith H. Turner
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jake Everett
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Urvish Trivedi
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Kendra P. Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Marvin Whiteley
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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49
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Abstract
The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.
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50
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Jackson AA, Gross MJ, Daniels EF, Hampton TH, Hammond JH, Vallet-Gely I, Dove SL, Stanton BA, Hogan DA. Anr and its activation by PlcH activity in Pseudomonas aeruginosa host colonization and virulence. J Bacteriol 2013; 195:3093-104. [PMID: 23667230 PMCID: PMC3697539 DOI: 10.1128/jb.02169-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/29/2013] [Indexed: 12/21/2022] Open
Abstract
Pseudomonas aeruginosa hemolytic phospholipase C (PlcH) degrades phosphatidylcholine (PC), an abundant lipid in cell membranes and lung surfactant. A ΔplcHR mutant, known to be defective in virulence in animal models, was less able to colonize epithelial cell monolayers and was defective in biofilm formation on plastic when grown in lung surfactant. Microarray analyses found that strains defective in PlcH production had lower levels of Anr-regulated transcripts than the wild type. PC degradation stimulated the Anr regulon in an Anr-dependent manner under conditions where Anr activity was submaximal because of the presence of oxygen. Two PC catabolites, choline and glycine betaine (GB), were sufficient to stimulate Anr activity, and their catabolism was required for Anr activation. The addition of choline or GB to glucose-containing medium did not alter Anr protein levels, growth rates, or respiratory activity, and Anr activation could not be attributed to the osmoprotectant functions of GB. The Δanr mutant was defective in virulence in a mouse pneumonia model. Several lines of evidence indicate that Anr is important for the colonization of biotic and abiotic surfaces in both P. aeruginosa PAO1 and PA14 and that increases in Anr activity resulted in enhanced biofilm formation. Our data suggest that PlcH activity promotes Anr activity in oxic environments and that Anr activity contributes to virulence, even in the acute infection phase, where low oxygen tensions are not expected. This finding highlights the relationships among in vivo bacterial metabolism, the activity of the oxygen-sensitive regulator Anr, and virulence.
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Affiliation(s)
- Angelyca A. Jackson
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Maegan J. Gross
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Emily F. Daniels
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire, USA
| | - John H. Hammond
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Isabelle Vallet-Gely
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Simon L. Dove
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire, USA
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